User: ariel.balter

gravatar for ariel.balter
ariel.balter130
Reputation:
130
Status:
Trusted
Location:
Last seen:
1 week, 1 day ago
Joined:
2 years, 1 month ago
Email:
a***********@gmail.com

Posts by ariel.balter

<prev • 56 results • page 1 of 6 • next >
0
votes
1
answer
177
views
1
answers
Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
... I hear ya. I thought it would be a more straightforward question. ...
written 12 days ago by ariel.balter130
0
votes
1
answer
177
views
1
answers
Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
... I added a bunch of detail to the question. Maybe that will help. ...
written 12 days ago by ariel.balter130
3
votes
1
answer
177
views
6 follow
1
answer
BWA or STAR for microbiome 16s multiple sequence alignment?
... I'm working with MISeq processed sequences of microbiome 16s samples. Is there any reason why I should use R tools like `msa` (Bioconductor) or `decipher` over NGS tools like `bwa` or `STAR`? Specifically, I'm using a [dada2](https://benjjneb.github.io/dada2/) workflow put out by the authors. My g ...
microbiome 16s alignment rna-seq written 12 days ago by ariel.balter130 • updated 11 days ago by Charles Warden5.5k
0
votes
5
answers
2.3k
views
5
answers
Answer: A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
... You can easily install both [rstudio](https://anaconda.org/r/rstudio) and [spyder](https://anaconda.org/anaconda/spyder) with conda without root access. You should also consider using Jupyter notebooks. You can install jupyter with conda as well. Caveats: 1) You need to install all the R packages ...
written 3 months ago by ariel.balter130
0
votes
1
answer
888
views
1
answers
Comment: C: samtools view by chromosome region chr:1000-1001000 creates "unknown reference n
... Yup! That did it. I thought I had tried that... Thanks! ...
written 17 months ago by ariel.balter130
0
votes
3
answers
6.8k
views
3
answers
Comment: C: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
... I don't see an equivalent to depth or bedcov in the [sambamba docs](http://lomereiter.github.io/sambamba/docs/sambamba-view.html) ...
written 17 months ago by ariel.balter130
3
votes
1
answer
888
views
1
answer
samtools view by chromosome region chr:1000-1001000 creates "unknown reference name" error
... I'm trying to create truncated versions of my bams for testing. The [samtools docs](http://www.htslib.org/doc/samtools.html) say: > REGIONS: > > Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. > > Important note: when multipl ...
samtools written 17 months ago by ariel.balter130 • updated 17 months ago by Pierre Lindenbaum113k
2
votes
0
answers
2.3k
views
0
answers
Comment: C: What is the definition of "read depth" vs "coverage"? (again...)
... NOOOOO! That is exactly what I did not want to hear :( ...
written 17 months ago by ariel.balter130
7
votes
0
answers
2.3k
views
6 follow
0
answers
What is the definition of "read depth" vs "coverage"? (again...)
... There are a number of biostars posts on how to calculate coverage and read depth, and what they mean. I'm still confused. This is how I currently understand things: ## Depth (or Read Depth) at a BP coordinate The number of "hits" on that coordinate resulting from alignment. In other words, the num ...
read depth coverage depth written 17 months ago by ariel.balter130
0
votes
0
answers
1.6k
views
0
answers
Comment: C: Typical costs for RNA-Seq analysis
... Looking at the first link, it's not very real-world informative. The prices range over an order of magnitude from $17/hour to $170/hour, and from $100/sample to $500/sample. AllSeq appears to be one of those services like if you search for "price for insurance" you get a website that tells you it wi ...
written 17 months ago by ariel.balter130

Latest awards to ariel.balter

Supporter 10 weeks ago, voted at least 25 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For Typical costs for RNA-Seq analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For MACS2 with multiple replicates
Popular Question 16 months ago, created a question with more than 1,000 views. For MACS2 Narrow peak (narrowPeak) output format
Popular Question 16 months ago, created a question with more than 1,000 views. For Difference between samtools DEPTH and MPILEUP
Popular Question 16 months ago, created a question with more than 1,000 views. For Can't get samtools version: "unrecognized command"
Popular Question 16 months ago, created a question with more than 1,000 views. For Relationship of bedGraph to wig.
Popular Question 16 months ago, created a question with more than 1,000 views. For Typical costs for RNA-Seq analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For Tophat and Bowtie installed with Conda not working on test data.
Popular Question 16 months ago, created a question with more than 1,000 views. For What does "pileup" mean in the context of MACS2 peak caller?
Popular Question 16 months ago, created a question with more than 1,000 views. For What is the definition of "read depth" vs "coverage"? (again...)
Student 16 months ago, asked a question with at least 3 up-votes. For Difference between samtools DEPTH and MPILEUP

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2257 users visited in the last hour